How to Clean Your VPS Server (Step-by-Step Guide for Beginners)

If your VPS has started running slowly, deployments are failing, or you're seeing messages like "No space left on device", don't panic. This guide will walk you through cleaning your server safely—even if you've never used Linux before.

We'll explain what each command does, why you're running it, and what to expect after running it.

Who is this guide for?

• Beginners using Ubuntu VPS
• Coolify users
• Docker users
• Anyone whose VPS is running out of storage

Before You Begin

What is a VPS?

A Virtual Private Server (VPS) is your own computer running in the cloud. It hosts your websites, applications, and databases.

Just like your laptop, your VPS collects temporary files, logs, unused downloads, and old application files over time.

Cleaning these files regularly keeps your server healthy.

Step 1: Connect to Your VPS

You first need to log into your server.

Windows (PowerShell)

Open PowerShell and type:

ssh root@YOUR_SERVER_IP

Example:

ssh root@123.45.67.89

Replace YOUR_SERVER_IP with your VPS IP address.

If this is your first time connecting, you'll see:

Type:

Then press Enter.

Enter your password if requested.

If you're using SSH keys, you'll log in automatically.

Step 2: Check How Much Storage Is Used

Before deleting anything, let's see how full the server is.

Run:

df -h

Example output:

What does this mean?

If your server is above 85%, it's a good idea to clean it.

Step 3: Find What's Using the Storage

Run:

du -h --max-depth=1 / 2>/dev/null | sort -hr | head -20

This command lists the biggest folders on your server.

Example:

Don't delete anything yet.

We're only identifying where the storage is being used.

Step 4: If You Use Docker or Coolify

Most developers using Coolify store applications inside Docker.

Check Docker's storage usage:

docker system df

Example:

Docker often consumes the most storage on a VPS.

Step 5: Clean Ubuntu Package Cache

Whenever Ubuntu installs software, it saves downloaded installation files.

These files are no longer needed after installation.

Run:

sudo apt clean

Nothing important is deleted.

Only temporary installation files are removed.

Step 6: Remove Old Packages

Sometimes Ubuntu keeps packages that are no longer being used.

Remove them:

sudo apt autoremove -y

This safely removes software that your system no longer needs.

Step 7: Clean Old System Logs

Every application writes logs.

Over months, they can grow into several gigabytes.

Check their size:

journalctl --disk-usage

Example:

Keep only the last seven days:

sudo journalctl --vacuum-time=7d

Or keep only 200MB:

sudo journalctl --vacuum-size=200M

Either option is perfectly fine.

Step 8: Remove Unused Docker Files

Docker stores:

• Old containers
• Old images
• Build cache
• Networks

Many of these are no longer needed.

Clean them:

docker system prune

Docker asks:

Type:

Press Enter.

If you don't want the confirmation:

docker system prune -f

Step 9: Remove Old Docker Images

If you've deployed your application many times, Docker keeps old versions.

Delete images that are no longer used:

docker system prune -a -f

This can free several gigabytes.

Your next deployment may take slightly longer because Docker downloads the images again.

Step 10: Clean Docker Build Cache

Every deployment creates build files.

These build files aren't needed forever.

Check cache size:

docker builder du

Then remove it:

docker builder prune -a -f

This is one of the easiest ways to recover storage.

Step 11: Check Docker Volumes (Important)

Volumes store your important data.

Examples:

• MongoDB
• PostgreSQL
• MySQL
• Redis
• Uploaded files
• Coolify data

View them:

docker volume ls

⚠️ Important

Do NOT run:

docker volume prune

unless you are 100% sure the volumes are no longer needed.

Deleting the wrong volume can permanently erase your database.

Step 12: Remove Large Docker Logs

Containers generate logs every second.

Find large logs:

find /var/lib/docker/containers/ -name "*-json.log" -exec du -h {} + | sort -hr | head

If a log file has become very large, clear it:

find /var/lib/docker/containers/ -name "*-json.log" -size +100M -exec truncate -s 0 {} \;

This clears the logs without stopping your applications.

Step 13: Check Coolify Backups

If you use Coolify, backups may occupy a lot of storage.

Check backup size:

du -sh /data/coolify/backups

Delete only backups you no longer need.

Always keep at least one recent backup.

Step 14: Check Your Storage Again

Now see how much storage you've recovered.

Run:

df -h

Compare it with the first result.

You should now have significantly more free space.

Step 15: Make Sure Everything Still Works

Check your running applications.

docker ps

You should see all your containers running.

Then open your website in a browser.

Make sure:

• Your website loads
• Login works
• Database works
• Images load
• Applications respond normally

If everything works, your cleanup was successful.

How Often Should You Clean Your VPS?

For most servers:

Common Mistakes to Avoid

❌ Deleting Docker volumes without checking them.

❌ Deleting random folders because they're large.

❌ Cleaning logs while debugging an issue.

❌ Removing backups before confirming you have another copy.

❌ Ignoring low disk space warnings.

Quick Cleanup Commands

If you're already comfortable with Linux, these commands perform the most common cleanup tasks:

df -h
docker system df
apt clean
apt autoclean
apt autoremove --dry-run
journalctl --vacuum-time=7d
docker system prune -a
docker builder prune -a
df -h
docker system df

Final Thoughts

Cleaning your VPS doesn't have to be intimidating. By following the steps in this guide, you can safely free up disk space, improve performance, and avoid common storage-related issues without risking your applications or data.

A good habit is to check your server's disk usage once a month and perform a cleanup whenever storage usage exceeds 80%. Regular maintenance keeps deployments smooth, applications responsive, and your VPS ready for future growth.

Whether you're hosting a personal portfolio, a business website, or multiple applications with Docker and Coolify, a little maintenance goes a long way toward keeping your server reliable.